Multiple sequence alignment - TraesCS3A01G083300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G083300 chr3A 100.000 2213 0 0 1 2213 53565920 53568132 0.000000e+00 4087.0
1 TraesCS3A01G083300 chr3A 96.833 221 3 3 1 218 632552092 632551873 1.250000e-97 366.0
2 TraesCS3A01G083300 chr3A 91.860 172 11 2 421 589 585298152 585297981 1.020000e-58 237.0
3 TraesCS3A01G083300 chr3B 88.902 1640 97 31 595 2181 65557856 65559463 0.000000e+00 1941.0
4 TraesCS3A01G083300 chr3B 92.857 210 5 1 215 424 65557640 65557839 1.660000e-76 296.0
5 TraesCS3A01G083300 chr3D 90.076 1048 43 25 589 1611 42090527 42089516 0.000000e+00 1303.0
6 TraesCS3A01G083300 chr3D 88.676 574 33 11 1664 2211 42089518 42088951 0.000000e+00 671.0
7 TraesCS3A01G083300 chr3D 96.429 224 7 1 1 224 74752442 74752220 3.470000e-98 368.0
8 TraesCS3A01G083300 chr3D 93.976 166 8 1 426 589 87925996 87926161 1.310000e-62 250.0
9 TraesCS3A01G083300 chr3D 84.615 208 20 7 1304 1506 600526806 600526606 1.730000e-46 196.0
10 TraesCS3A01G083300 chr3D 94.595 74 3 1 309 381 42090655 42090582 1.800000e-21 113.0
11 TraesCS3A01G083300 chr7A 82.731 747 79 29 1300 2020 681252198 681251476 8.680000e-174 619.0
12 TraesCS3A01G083300 chr7A 96.347 219 6 2 1 218 67506812 67507029 2.090000e-95 359.0
13 TraesCS3A01G083300 chr2A 97.738 221 3 2 1 220 598345651 598345870 1.600000e-101 379.0
14 TraesCS3A01G083300 chr2A 96.789 218 6 1 1 218 684249822 684250038 1.620000e-96 363.0
15 TraesCS3A01G083300 chr2A 93.373 166 9 1 426 589 184561319 184561154 6.100000e-61 244.0
16 TraesCS3A01G083300 chr2A 83.824 204 21 7 1304 1502 88089925 88090121 1.350000e-42 183.0
17 TraesCS3A01G083300 chr2A 83.240 179 14 13 1298 1468 712969699 712969869 1.370000e-32 150.0
18 TraesCS3A01G083300 chr2A 81.215 181 34 0 1006 1186 679982439 679982259 1.770000e-31 147.0
19 TraesCS3A01G083300 chr2A 98.551 69 1 0 215 283 100226099 100226167 2.980000e-24 122.0
20 TraesCS3A01G083300 chr7D 97.706 218 4 1 1 218 574026846 574027062 7.460000e-100 374.0
21 TraesCS3A01G083300 chr4A 96.789 218 6 1 1 218 636063244 636063028 1.620000e-96 363.0
22 TraesCS3A01G083300 chr1D 96.364 220 6 2 1 219 445319712 445319494 5.810000e-96 361.0
23 TraesCS3A01G083300 chr1D 80.663 181 19 7 1563 1731 446304974 446304798 2.310000e-25 126.0
24 TraesCS3A01G083300 chr1D 92.500 40 0 3 1942 1981 66379401 66379437 1.000000e-03 54.7
25 TraesCS3A01G083300 chr5D 95.946 222 8 1 1 222 59392120 59391900 2.090000e-95 359.0
26 TraesCS3A01G083300 chr5D 91.860 172 11 3 430 600 396457767 396457936 1.020000e-58 237.0
27 TraesCS3A01G083300 chr5D 82.320 181 17 8 1298 1468 468189171 468188996 2.290000e-30 143.0
28 TraesCS3A01G083300 chr5D 82.320 181 17 8 1298 1468 468343323 468343498 2.290000e-30 143.0
29 TraesCS3A01G083300 chr5D 96.970 33 0 1 1949 1981 216979813 216979782 1.000000e-03 54.7
30 TraesCS3A01G083300 chr5A 93.491 169 9 1 424 590 320214238 320214406 1.310000e-62 250.0
31 TraesCS3A01G083300 chr5A 84.831 178 12 9 1298 1468 34524038 34523869 4.890000e-37 165.0
32 TraesCS3A01G083300 chr6D 93.902 164 8 1 429 590 145462625 145462462 1.700000e-61 246.0
33 TraesCS3A01G083300 chr6D 90.503 179 13 3 430 606 351233596 351233420 1.320000e-57 233.0
34 TraesCS3A01G083300 chr6B 92.857 168 10 1 425 590 172738366 172738533 2.200000e-60 243.0
35 TraesCS3A01G083300 chr4D 90.110 182 13 4 427 605 479687257 479687436 4.750000e-57 231.0
36 TraesCS3A01G083300 chr4D 82.486 177 16 8 1298 1464 318745093 318745264 8.240000e-30 141.0
37 TraesCS3A01G083300 chr4D 92.500 40 1 2 1942 1981 488483162 488483199 3.070000e-04 56.5
38 TraesCS3A01G083300 chr2D 85.854 205 17 7 1304 1503 22798149 22798346 8.010000e-50 207.0
39 TraesCS3A01G083300 chr2D 80.105 191 38 0 996 1186 537448409 537448219 2.290000e-30 143.0
40 TraesCS3A01G083300 chr2D 80.978 184 17 10 1297 1470 618341391 618341566 1.780000e-26 130.0
41 TraesCS3A01G083300 chr1A 83.824 204 21 7 1304 1502 532360475 532360279 1.350000e-42 183.0
42 TraesCS3A01G083300 chr1A 81.768 181 17 7 1560 1728 5865990 5866166 1.070000e-28 137.0
43 TraesCS3A01G083300 chr1A 78.689 183 22 11 1297 1470 117166496 117166670 3.010000e-19 106.0
44 TraesCS3A01G083300 chr2B 81.215 181 34 0 1006 1186 640085916 640085736 1.770000e-31 147.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G083300 chr3A 53565920 53568132 2212 False 4087.000000 4087 100.000000 1 2213 1 chr3A.!!$F1 2212
1 TraesCS3A01G083300 chr3B 65557640 65559463 1823 False 1118.500000 1941 90.879500 215 2181 2 chr3B.!!$F1 1966
2 TraesCS3A01G083300 chr3D 42088951 42090655 1704 True 695.666667 1303 91.115667 309 2211 3 chr3D.!!$R3 1902
3 TraesCS3A01G083300 chr7A 681251476 681252198 722 True 619.000000 619 82.731000 1300 2020 1 chr7A.!!$R1 720

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
147 148 0.029834 CTTGGTGTGTTGTGCTGCTC 59.970 55.0 0.00 0.00 0.00 4.26 F
782 827 0.174845 AATGATGGCATGTGCAGCAC 59.825 50.0 19.37 19.37 44.36 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1174 0.031314 CGGAGTGGACGATGATGGAG 59.969 60.0 0.0 0.0 0.0 3.86 R
1897 1984 0.393077 CTCGACACCAAACCCTCTGT 59.607 55.0 0.0 0.0 0.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.793946 GTGCTGCTTGGTATGCGG 59.206 61.111 0.00 0.00 39.61 5.69
20 21 3.576356 CTGCTTGGTATGCGGCGG 61.576 66.667 9.78 0.00 0.00 6.13
21 22 4.089239 TGCTTGGTATGCGGCGGA 62.089 61.111 9.78 6.17 0.00 5.54
22 23 2.591715 GCTTGGTATGCGGCGGAT 60.592 61.111 19.81 19.81 0.00 4.18
23 24 2.607892 GCTTGGTATGCGGCGGATC 61.608 63.158 19.45 9.65 0.00 3.36
24 25 2.279851 TTGGTATGCGGCGGATCG 60.280 61.111 19.45 0.00 0.00 3.69
25 26 3.800685 TTGGTATGCGGCGGATCGG 62.801 63.158 19.45 0.00 0.00 4.18
26 27 3.986006 GGTATGCGGCGGATCGGA 61.986 66.667 19.45 0.00 34.52 4.55
27 28 2.430921 GTATGCGGCGGATCGGAG 60.431 66.667 19.45 0.00 33.32 4.63
28 29 4.357947 TATGCGGCGGATCGGAGC 62.358 66.667 19.45 9.03 33.32 4.70
34 35 4.162690 GCGGATCGGAGCCTTGGT 62.163 66.667 10.99 0.00 0.00 3.67
35 36 2.107141 CGGATCGGAGCCTTGGTC 59.893 66.667 10.99 0.00 0.00 4.02
36 37 2.427245 CGGATCGGAGCCTTGGTCT 61.427 63.158 10.99 0.00 0.00 3.85
37 38 1.144936 GGATCGGAGCCTTGGTCTG 59.855 63.158 4.74 0.00 37.73 3.51
38 39 1.617947 GGATCGGAGCCTTGGTCTGT 61.618 60.000 4.74 0.00 37.64 3.41
39 40 0.460987 GATCGGAGCCTTGGTCTGTG 60.461 60.000 2.42 0.00 37.64 3.66
40 41 1.903877 ATCGGAGCCTTGGTCTGTGG 61.904 60.000 2.42 0.00 37.64 4.17
41 42 2.883828 CGGAGCCTTGGTCTGTGGT 61.884 63.158 0.00 0.00 32.48 4.16
42 43 1.302832 GGAGCCTTGGTCTGTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
43 44 1.754745 GAGCCTTGGTCTGTGGTGA 59.245 57.895 0.00 0.00 0.00 4.02
44 45 0.326264 GAGCCTTGGTCTGTGGTGAT 59.674 55.000 0.00 0.00 0.00 3.06
45 46 0.773644 AGCCTTGGTCTGTGGTGATT 59.226 50.000 0.00 0.00 0.00 2.57
46 47 1.145738 AGCCTTGGTCTGTGGTGATTT 59.854 47.619 0.00 0.00 0.00 2.17
47 48 1.270550 GCCTTGGTCTGTGGTGATTTG 59.729 52.381 0.00 0.00 0.00 2.32
48 49 2.586425 CCTTGGTCTGTGGTGATTTGT 58.414 47.619 0.00 0.00 0.00 2.83
49 50 2.294233 CCTTGGTCTGTGGTGATTTGTG 59.706 50.000 0.00 0.00 0.00 3.33
50 51 2.727123 TGGTCTGTGGTGATTTGTGT 57.273 45.000 0.00 0.00 0.00 3.72
51 52 2.571212 TGGTCTGTGGTGATTTGTGTC 58.429 47.619 0.00 0.00 0.00 3.67
52 53 1.880027 GGTCTGTGGTGATTTGTGTCC 59.120 52.381 0.00 0.00 0.00 4.02
53 54 1.531149 GTCTGTGGTGATTTGTGTCCG 59.469 52.381 0.00 0.00 0.00 4.79
54 55 0.874390 CTGTGGTGATTTGTGTCCGG 59.126 55.000 0.00 0.00 0.00 5.14
55 56 0.181587 TGTGGTGATTTGTGTCCGGT 59.818 50.000 0.00 0.00 0.00 5.28
56 57 0.591170 GTGGTGATTTGTGTCCGGTG 59.409 55.000 0.00 0.00 0.00 4.94
57 58 0.536233 TGGTGATTTGTGTCCGGTGG 60.536 55.000 0.00 0.00 0.00 4.61
58 59 1.241315 GGTGATTTGTGTCCGGTGGG 61.241 60.000 0.00 0.00 0.00 4.61
59 60 1.602323 TGATTTGTGTCCGGTGGGC 60.602 57.895 0.00 0.00 0.00 5.36
60 61 2.671619 ATTTGTGTCCGGTGGGCG 60.672 61.111 0.00 0.00 0.00 6.13
88 89 4.179579 GGGTCATCCGCGCTTTGC 62.180 66.667 5.56 0.00 41.47 3.68
89 90 4.179579 GGTCATCCGCGCTTTGCC 62.180 66.667 5.56 2.72 42.08 4.52
90 91 3.430862 GTCATCCGCGCTTTGCCA 61.431 61.111 5.56 0.00 42.08 4.92
91 92 2.671276 TCATCCGCGCTTTGCCAA 60.671 55.556 5.56 0.00 42.08 4.52
92 93 2.202518 CATCCGCGCTTTGCCAAG 60.203 61.111 5.56 0.00 42.08 3.61
100 101 2.049802 CTTTGCCAAGCTGCCGTG 60.050 61.111 0.00 0.00 0.00 4.94
101 102 3.562779 CTTTGCCAAGCTGCCGTGG 62.563 63.158 14.06 14.06 42.66 4.94
102 103 4.892965 TTGCCAAGCTGCCGTGGT 62.893 61.111 18.16 0.00 41.91 4.16
103 104 4.892965 TGCCAAGCTGCCGTGGTT 62.893 61.111 18.16 0.00 41.91 3.67
104 105 4.347453 GCCAAGCTGCCGTGGTTG 62.347 66.667 18.16 6.69 41.91 3.77
114 115 3.677002 CCGTGGTTGGCATTTGTTT 57.323 47.368 0.00 0.00 0.00 2.83
115 116 1.496934 CCGTGGTTGGCATTTGTTTC 58.503 50.000 0.00 0.00 0.00 2.78
116 117 1.068434 CCGTGGTTGGCATTTGTTTCT 59.932 47.619 0.00 0.00 0.00 2.52
117 118 2.482839 CCGTGGTTGGCATTTGTTTCTT 60.483 45.455 0.00 0.00 0.00 2.52
118 119 2.794350 CGTGGTTGGCATTTGTTTCTTC 59.206 45.455 0.00 0.00 0.00 2.87
119 120 3.490761 CGTGGTTGGCATTTGTTTCTTCT 60.491 43.478 0.00 0.00 0.00 2.85
120 121 4.441792 GTGGTTGGCATTTGTTTCTTCTT 58.558 39.130 0.00 0.00 0.00 2.52
121 122 4.507756 GTGGTTGGCATTTGTTTCTTCTTC 59.492 41.667 0.00 0.00 0.00 2.87
122 123 4.405358 TGGTTGGCATTTGTTTCTTCTTCT 59.595 37.500 0.00 0.00 0.00 2.85
123 124 5.104982 TGGTTGGCATTTGTTTCTTCTTCTT 60.105 36.000 0.00 0.00 0.00 2.52
124 125 5.817296 GGTTGGCATTTGTTTCTTCTTCTTT 59.183 36.000 0.00 0.00 0.00 2.52
125 126 6.316140 GGTTGGCATTTGTTTCTTCTTCTTTT 59.684 34.615 0.00 0.00 0.00 2.27
126 127 7.148255 GGTTGGCATTTGTTTCTTCTTCTTTTT 60.148 33.333 0.00 0.00 0.00 1.94
143 144 3.951775 TTTTTCTTGGTGTGTTGTGCT 57.048 38.095 0.00 0.00 0.00 4.40
144 145 2.937469 TTTCTTGGTGTGTTGTGCTG 57.063 45.000 0.00 0.00 0.00 4.41
145 146 0.455410 TTCTTGGTGTGTTGTGCTGC 59.545 50.000 0.00 0.00 0.00 5.25
146 147 0.394216 TCTTGGTGTGTTGTGCTGCT 60.394 50.000 0.00 0.00 0.00 4.24
147 148 0.029834 CTTGGTGTGTTGTGCTGCTC 59.970 55.000 0.00 0.00 0.00 4.26
148 149 1.713937 TTGGTGTGTTGTGCTGCTCG 61.714 55.000 0.00 0.00 0.00 5.03
149 150 2.051882 GTGTGTTGTGCTGCTCGC 60.052 61.111 0.00 0.00 39.77 5.03
150 151 3.279116 TGTGTTGTGCTGCTCGCC 61.279 61.111 0.00 0.00 38.05 5.54
151 152 3.279116 GTGTTGTGCTGCTCGCCA 61.279 61.111 0.00 0.00 38.05 5.69
152 153 3.279116 TGTTGTGCTGCTCGCCAC 61.279 61.111 0.00 0.00 38.05 5.01
153 154 3.279116 GTTGTGCTGCTCGCCACA 61.279 61.111 0.00 0.00 38.05 4.17
154 155 2.974148 TTGTGCTGCTCGCCACAG 60.974 61.111 0.00 0.00 38.05 3.66
167 168 2.295253 GCCACAGCGTTATCTGTACT 57.705 50.000 0.00 0.00 44.81 2.73
168 169 2.194271 GCCACAGCGTTATCTGTACTC 58.806 52.381 0.00 0.00 44.81 2.59
169 170 2.451132 CCACAGCGTTATCTGTACTCG 58.549 52.381 0.00 0.00 44.81 4.18
170 171 2.096980 CCACAGCGTTATCTGTACTCGA 59.903 50.000 0.00 0.00 44.81 4.04
171 172 3.243101 CCACAGCGTTATCTGTACTCGAT 60.243 47.826 0.00 0.00 44.81 3.59
172 173 3.726235 CACAGCGTTATCTGTACTCGATG 59.274 47.826 8.04 0.00 44.81 3.84
173 174 3.377485 ACAGCGTTATCTGTACTCGATGT 59.623 43.478 0.00 0.00 44.77 3.06
174 175 4.142447 ACAGCGTTATCTGTACTCGATGTT 60.142 41.667 0.00 0.00 45.98 2.71
175 176 4.205181 CAGCGTTATCTGTACTCGATGTTG 59.795 45.833 8.04 0.00 34.14 3.33
176 177 3.486108 GCGTTATCTGTACTCGATGTTGG 59.514 47.826 8.04 0.00 0.00 3.77
177 178 4.669318 CGTTATCTGTACTCGATGTTGGT 58.331 43.478 8.04 0.00 0.00 3.67
178 179 5.100259 CGTTATCTGTACTCGATGTTGGTT 58.900 41.667 8.04 0.00 0.00 3.67
179 180 5.004440 CGTTATCTGTACTCGATGTTGGTTG 59.996 44.000 8.04 0.00 0.00 3.77
180 181 2.683968 TCTGTACTCGATGTTGGTTGC 58.316 47.619 0.00 0.00 0.00 4.17
181 182 2.299013 TCTGTACTCGATGTTGGTTGCT 59.701 45.455 0.00 0.00 0.00 3.91
182 183 3.067106 CTGTACTCGATGTTGGTTGCTT 58.933 45.455 0.00 0.00 0.00 3.91
183 184 3.472652 TGTACTCGATGTTGGTTGCTTT 58.527 40.909 0.00 0.00 0.00 3.51
184 185 3.249799 TGTACTCGATGTTGGTTGCTTTG 59.750 43.478 0.00 0.00 0.00 2.77
185 186 1.608590 ACTCGATGTTGGTTGCTTTGG 59.391 47.619 0.00 0.00 0.00 3.28
186 187 1.879380 CTCGATGTTGGTTGCTTTGGA 59.121 47.619 0.00 0.00 0.00 3.53
187 188 2.293122 CTCGATGTTGGTTGCTTTGGAA 59.707 45.455 0.00 0.00 0.00 3.53
188 189 2.890311 TCGATGTTGGTTGCTTTGGAAT 59.110 40.909 0.00 0.00 0.00 3.01
189 190 4.075682 TCGATGTTGGTTGCTTTGGAATA 58.924 39.130 0.00 0.00 0.00 1.75
190 191 4.083003 TCGATGTTGGTTGCTTTGGAATAC 60.083 41.667 0.00 0.00 0.00 1.89
191 192 4.320861 CGATGTTGGTTGCTTTGGAATACA 60.321 41.667 0.00 0.00 0.00 2.29
192 193 5.537188 GATGTTGGTTGCTTTGGAATACAA 58.463 37.500 0.00 0.00 37.28 2.41
193 194 5.344743 TGTTGGTTGCTTTGGAATACAAA 57.655 34.783 0.00 0.00 46.34 2.83
200 201 1.551452 TTTGGAATACAAAGCGGGGG 58.449 50.000 0.00 0.00 43.81 5.40
201 202 0.699399 TTGGAATACAAAGCGGGGGA 59.301 50.000 0.00 0.00 35.79 4.81
202 203 0.699399 TGGAATACAAAGCGGGGGAA 59.301 50.000 0.00 0.00 0.00 3.97
203 204 1.075698 TGGAATACAAAGCGGGGGAAA 59.924 47.619 0.00 0.00 0.00 3.13
204 205 1.475280 GGAATACAAAGCGGGGGAAAC 59.525 52.381 0.00 0.00 0.00 2.78
245 246 5.432645 TGGTATGTTGTGAGACAGAAACAA 58.567 37.500 0.00 0.00 36.23 2.83
256 257 4.712476 AGACAGAAACAAGAATCAGTGCT 58.288 39.130 0.00 0.00 0.00 4.40
320 321 8.352942 CCTTAATTTATTCTACACCAGATTGGC 58.647 37.037 0.00 0.00 42.67 4.52
377 414 7.175467 TGTGAGACAGAAAAACATGAATAGCAT 59.825 33.333 0.00 0.00 37.85 3.79
419 456 3.242870 GCCATACTTGTTGCTACATCTGC 60.243 47.826 0.81 0.00 33.44 4.26
424 461 2.284754 TGTTGCTACATCTGCCCAAA 57.715 45.000 0.00 0.00 0.00 3.28
426 463 3.961849 TGTTGCTACATCTGCCCAAATA 58.038 40.909 0.00 0.00 0.00 1.40
428 465 4.338964 TGTTGCTACATCTGCCCAAATATG 59.661 41.667 0.00 0.00 0.00 1.78
429 466 4.169059 TGCTACATCTGCCCAAATATGT 57.831 40.909 0.00 0.00 36.56 2.29
431 468 5.063204 TGCTACATCTGCCCAAATATGTAC 58.937 41.667 0.00 0.00 34.54 2.90
432 469 5.163205 TGCTACATCTGCCCAAATATGTACT 60.163 40.000 0.00 0.00 34.54 2.73
434 471 4.718961 ACATCTGCCCAAATATGTACTCC 58.281 43.478 0.00 0.00 30.99 3.85
435 472 3.857157 TCTGCCCAAATATGTACTCCC 57.143 47.619 0.00 0.00 0.00 4.30
437 474 3.391296 TCTGCCCAAATATGTACTCCCTC 59.609 47.826 0.00 0.00 0.00 4.30
438 475 2.441750 TGCCCAAATATGTACTCCCTCC 59.558 50.000 0.00 0.00 0.00 4.30
439 476 2.550208 GCCCAAATATGTACTCCCTCCG 60.550 54.545 0.00 0.00 0.00 4.63
440 477 2.704065 CCCAAATATGTACTCCCTCCGT 59.296 50.000 0.00 0.00 0.00 4.69
441 478 3.135895 CCCAAATATGTACTCCCTCCGTT 59.864 47.826 0.00 0.00 0.00 4.44
442 479 4.377897 CCAAATATGTACTCCCTCCGTTC 58.622 47.826 0.00 0.00 0.00 3.95
443 480 4.377897 CAAATATGTACTCCCTCCGTTCC 58.622 47.826 0.00 0.00 0.00 3.62
444 481 3.614568 ATATGTACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
445 482 4.736611 ATATGTACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
446 483 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
447 484 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
448 485 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
449 486 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
450 487 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
451 488 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
452 489 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
453 490 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
454 491 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
455 492 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
456 493 5.242393 TCCCTCCGTTCCTAAATATAAGTCG 59.758 44.000 0.00 0.00 0.00 4.18
457 494 5.010415 CCCTCCGTTCCTAAATATAAGTCGT 59.990 44.000 0.00 0.00 0.00 4.34
458 495 6.462067 CCCTCCGTTCCTAAATATAAGTCGTT 60.462 42.308 0.00 0.00 0.00 3.85
459 496 6.982724 CCTCCGTTCCTAAATATAAGTCGTTT 59.017 38.462 0.00 0.00 0.00 3.60
460 497 7.493645 CCTCCGTTCCTAAATATAAGTCGTTTT 59.506 37.037 0.00 0.00 0.00 2.43
461 498 9.520204 CTCCGTTCCTAAATATAAGTCGTTTTA 57.480 33.333 0.00 0.00 0.00 1.52
462 499 9.520204 TCCGTTCCTAAATATAAGTCGTTTTAG 57.480 33.333 0.00 0.00 33.47 1.85
463 500 9.520204 CCGTTCCTAAATATAAGTCGTTTTAGA 57.480 33.333 0.00 0.00 34.90 2.10
478 515 9.968870 AGTCGTTTTAGAGATTCCAATATAGAC 57.031 33.333 0.00 0.00 0.00 2.59
479 516 9.968870 GTCGTTTTAGAGATTCCAATATAGACT 57.031 33.333 0.00 0.00 0.00 3.24
487 524 9.179909 AGAGATTCCAATATAGACTACATACGG 57.820 37.037 0.00 0.00 0.00 4.02
488 525 9.175312 GAGATTCCAATATAGACTACATACGGA 57.825 37.037 0.00 0.00 0.00 4.69
489 526 9.179909 AGATTCCAATATAGACTACATACGGAG 57.820 37.037 0.00 0.00 0.00 4.63
490 527 6.754702 TCCAATATAGACTACATACGGAGC 57.245 41.667 0.00 0.00 0.00 4.70
491 528 6.243148 TCCAATATAGACTACATACGGAGCA 58.757 40.000 0.00 0.00 0.00 4.26
492 529 6.717997 TCCAATATAGACTACATACGGAGCAA 59.282 38.462 0.00 0.00 0.00 3.91
493 530 7.231925 TCCAATATAGACTACATACGGAGCAAA 59.768 37.037 0.00 0.00 0.00 3.68
494 531 7.870954 CCAATATAGACTACATACGGAGCAAAA 59.129 37.037 0.00 0.00 0.00 2.44
495 532 9.424319 CAATATAGACTACATACGGAGCAAAAT 57.576 33.333 0.00 0.00 0.00 1.82
496 533 8.988064 ATATAGACTACATACGGAGCAAAATG 57.012 34.615 0.00 0.00 0.00 2.32
497 534 5.339008 AGACTACATACGGAGCAAAATGA 57.661 39.130 0.00 0.00 0.00 2.57
498 535 5.352284 AGACTACATACGGAGCAAAATGAG 58.648 41.667 0.00 0.00 0.00 2.90
499 536 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
500 537 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
501 538 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
502 539 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
503 540 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
504 541 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
505 542 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
506 543 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
507 544 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
508 545 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
509 546 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
554 591 9.778741 ACATCCGTATGTAGTTCATATTGAAAT 57.221 29.630 0.00 0.00 44.66 2.17
557 594 9.692749 TCCGTATGTAGTTCATATTGAAATCTC 57.307 33.333 0.00 0.00 38.22 2.75
558 595 9.698309 CCGTATGTAGTTCATATTGAAATCTCT 57.302 33.333 0.00 0.00 38.22 3.10
579 616 8.433421 TCTCTAAAAAGGCATATTTAGGAACG 57.567 34.615 13.27 0.00 38.85 3.95
580 617 7.497909 TCTCTAAAAAGGCATATTTAGGAACGG 59.502 37.037 13.27 4.23 38.85 4.44
581 618 7.340256 TCTAAAAAGGCATATTTAGGAACGGA 58.660 34.615 13.27 0.00 38.85 4.69
582 619 6.451064 AAAAAGGCATATTTAGGAACGGAG 57.549 37.500 0.00 0.00 0.00 4.63
583 620 3.771577 AGGCATATTTAGGAACGGAGG 57.228 47.619 0.00 0.00 0.00 4.30
584 621 3.314693 AGGCATATTTAGGAACGGAGGA 58.685 45.455 0.00 0.00 0.00 3.71
585 622 3.714798 AGGCATATTTAGGAACGGAGGAA 59.285 43.478 0.00 0.00 0.00 3.36
586 623 4.065789 GGCATATTTAGGAACGGAGGAAG 58.934 47.826 0.00 0.00 0.00 3.46
587 624 4.444449 GGCATATTTAGGAACGGAGGAAGT 60.444 45.833 0.00 0.00 0.00 3.01
588 625 5.221581 GGCATATTTAGGAACGGAGGAAGTA 60.222 44.000 0.00 0.00 0.00 2.24
589 626 6.465084 GCATATTTAGGAACGGAGGAAGTAT 58.535 40.000 0.00 0.00 0.00 2.12
590 627 6.590677 GCATATTTAGGAACGGAGGAAGTATC 59.409 42.308 0.00 0.00 0.00 2.24
591 628 5.548181 ATTTAGGAACGGAGGAAGTATCC 57.452 43.478 0.00 0.00 46.98 2.59
663 707 2.437413 CCTTTCTAACTGCCTCCAACC 58.563 52.381 0.00 0.00 0.00 3.77
678 722 0.597377 CAACCGCCCAAGTGAAAAGC 60.597 55.000 0.00 0.00 0.00 3.51
782 827 0.174845 AATGATGGCATGTGCAGCAC 59.825 50.000 19.37 19.37 44.36 4.40
866 915 3.438087 GGCCATTATATAGCACTGCACAG 59.562 47.826 0.00 0.00 0.00 3.66
937 986 1.338105 TGCAGTGTGTCAGAGCATACC 60.338 52.381 0.00 0.00 32.00 2.73
955 1004 3.848978 ACCCTGTTCTACCTTAGGAGT 57.151 47.619 4.77 0.00 31.91 3.85
956 1005 3.710724 ACCCTGTTCTACCTTAGGAGTC 58.289 50.000 4.77 0.00 31.91 3.36
957 1006 3.077088 ACCCTGTTCTACCTTAGGAGTCA 59.923 47.826 4.77 2.67 31.91 3.41
958 1007 4.094476 CCCTGTTCTACCTTAGGAGTCAA 58.906 47.826 4.77 0.00 31.91 3.18
959 1008 4.160626 CCCTGTTCTACCTTAGGAGTCAAG 59.839 50.000 4.77 0.00 31.91 3.02
960 1009 5.017490 CCTGTTCTACCTTAGGAGTCAAGA 58.983 45.833 4.77 0.00 31.91 3.02
962 1011 6.350612 CCTGTTCTACCTTAGGAGTCAAGAAG 60.351 46.154 4.77 0.00 31.91 2.85
963 1012 6.312529 TGTTCTACCTTAGGAGTCAAGAAGA 58.687 40.000 4.77 2.11 0.00 2.87
964 1013 6.434652 TGTTCTACCTTAGGAGTCAAGAAGAG 59.565 42.308 4.77 0.00 0.00 2.85
977 1026 7.023171 AGTCAAGAAGAGTAGAAGGTAGAGA 57.977 40.000 0.00 0.00 0.00 3.10
981 1030 7.181305 TCAAGAAGAGTAGAAGGTAGAGAGAGA 59.819 40.741 0.00 0.00 0.00 3.10
984 1033 6.732896 AGAGTAGAAGGTAGAGAGAGAGAG 57.267 45.833 0.00 0.00 0.00 3.20
985 1034 6.203072 AGAGTAGAAGGTAGAGAGAGAGAGT 58.797 44.000 0.00 0.00 0.00 3.24
986 1035 6.098409 AGAGTAGAAGGTAGAGAGAGAGAGTG 59.902 46.154 0.00 0.00 0.00 3.51
987 1036 5.962031 AGTAGAAGGTAGAGAGAGAGAGTGA 59.038 44.000 0.00 0.00 0.00 3.41
988 1037 5.359194 AGAAGGTAGAGAGAGAGAGTGAG 57.641 47.826 0.00 0.00 0.00 3.51
989 1038 4.164221 AGAAGGTAGAGAGAGAGAGTGAGG 59.836 50.000 0.00 0.00 0.00 3.86
990 1039 2.777692 AGGTAGAGAGAGAGAGTGAGGG 59.222 54.545 0.00 0.00 0.00 4.30
991 1040 2.158667 GGTAGAGAGAGAGAGTGAGGGG 60.159 59.091 0.00 0.00 0.00 4.79
992 1041 0.926293 AGAGAGAGAGAGTGAGGGGG 59.074 60.000 0.00 0.00 0.00 5.40
1125 1174 4.980805 TTCCACACCAGCGCCGTC 62.981 66.667 2.29 0.00 0.00 4.79
1238 1287 2.348660 ACTCGGTGTTTCGTGTTTTCA 58.651 42.857 0.00 0.00 33.88 2.69
1239 1288 2.743126 ACTCGGTGTTTCGTGTTTTCAA 59.257 40.909 0.00 0.00 33.88 2.69
1298 1349 6.062749 GGTTCTCTGAAAGTTTAGGGTCTTT 58.937 40.000 0.00 0.00 36.72 2.52
1451 1504 4.702131 AGCTCTGTTTCTGTGACACTTTTT 59.298 37.500 7.20 0.00 0.00 1.94
1604 1675 0.966179 GGTGCGGGAAAGGAACAAAT 59.034 50.000 0.00 0.00 0.00 2.32
1647 1718 1.678123 CCAGCTGAGGGTGAGTGAATG 60.678 57.143 17.39 0.00 42.91 2.67
1705 1776 3.003793 GTGAAGAACTGAGCCTGGTTTTC 59.996 47.826 0.00 0.00 0.00 2.29
1895 1982 2.738314 GTCGGGTAAAATGTGCGTAGTT 59.262 45.455 0.00 0.00 0.00 2.24
1897 1984 4.388469 GTCGGGTAAAATGTGCGTAGTTAA 59.612 41.667 0.00 0.00 0.00 2.01
1898 1985 4.388469 TCGGGTAAAATGTGCGTAGTTAAC 59.612 41.667 0.00 0.00 0.00 2.01
1991 2087 2.303311 AGCCTTCTTTCTGGGTAGTGAC 59.697 50.000 0.00 0.00 31.66 3.67
2022 2118 6.019108 AGGAAAGGAACAAAATCCAGCTTAT 58.981 36.000 0.00 0.00 42.27 1.73
2066 2169 3.369756 CAGGAATAAAAACGTCGCTGCTA 59.630 43.478 0.00 0.00 0.00 3.49
2104 2214 3.629855 TGTGTGTGTGTAAATTGGTCTGG 59.370 43.478 0.00 0.00 0.00 3.86
2108 2218 3.568007 TGTGTGTAAATTGGTCTGGAAGC 59.432 43.478 0.00 0.00 0.00 3.86
2109 2219 3.568007 GTGTGTAAATTGGTCTGGAAGCA 59.432 43.478 0.00 0.00 0.00 3.91
2194 2316 8.469200 AGTGATTCAGAGAGTTATTCAGAGAAG 58.531 37.037 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.793946 CCGCATACCAAGCAGCAC 59.206 61.111 0.00 0.00 0.00 4.40
2 3 4.241999 CGCCGCATACCAAGCAGC 62.242 66.667 0.00 0.00 32.24 5.25
3 4 3.576356 CCGCCGCATACCAAGCAG 61.576 66.667 0.00 0.00 0.00 4.24
4 5 3.399105 ATCCGCCGCATACCAAGCA 62.399 57.895 0.00 0.00 0.00 3.91
5 6 2.591715 ATCCGCCGCATACCAAGC 60.592 61.111 0.00 0.00 0.00 4.01
6 7 2.310233 CGATCCGCCGCATACCAAG 61.310 63.158 0.00 0.00 0.00 3.61
7 8 2.279851 CGATCCGCCGCATACCAA 60.280 61.111 0.00 0.00 0.00 3.67
8 9 4.293648 CCGATCCGCCGCATACCA 62.294 66.667 0.00 0.00 0.00 3.25
9 10 3.916392 CTCCGATCCGCCGCATACC 62.916 68.421 0.00 0.00 0.00 2.73
10 11 2.430921 CTCCGATCCGCCGCATAC 60.431 66.667 0.00 0.00 0.00 2.39
11 12 4.357947 GCTCCGATCCGCCGCATA 62.358 66.667 0.00 0.00 0.00 3.14
16 17 4.918201 CCAAGGCTCCGATCCGCC 62.918 72.222 7.13 7.13 46.65 6.13
17 18 4.162690 ACCAAGGCTCCGATCCGC 62.163 66.667 0.00 0.00 0.00 5.54
18 19 2.107141 GACCAAGGCTCCGATCCG 59.893 66.667 0.00 0.00 0.00 4.18
19 20 1.144936 CAGACCAAGGCTCCGATCC 59.855 63.158 0.00 0.00 0.00 3.36
20 21 0.460987 CACAGACCAAGGCTCCGATC 60.461 60.000 0.00 0.00 0.00 3.69
21 22 1.599047 CACAGACCAAGGCTCCGAT 59.401 57.895 0.00 0.00 0.00 4.18
22 23 2.583441 CCACAGACCAAGGCTCCGA 61.583 63.158 0.00 0.00 0.00 4.55
23 24 2.046892 CCACAGACCAAGGCTCCG 60.047 66.667 0.00 0.00 0.00 4.63
24 25 1.302832 CACCACAGACCAAGGCTCC 60.303 63.158 0.00 0.00 0.00 4.70
25 26 0.326264 ATCACCACAGACCAAGGCTC 59.674 55.000 0.00 0.00 0.00 4.70
26 27 0.773644 AATCACCACAGACCAAGGCT 59.226 50.000 0.00 0.00 0.00 4.58
27 28 1.270550 CAAATCACCACAGACCAAGGC 59.729 52.381 0.00 0.00 0.00 4.35
28 29 2.294233 CACAAATCACCACAGACCAAGG 59.706 50.000 0.00 0.00 0.00 3.61
29 30 2.951642 ACACAAATCACCACAGACCAAG 59.048 45.455 0.00 0.00 0.00 3.61
30 31 2.948979 GACACAAATCACCACAGACCAA 59.051 45.455 0.00 0.00 0.00 3.67
31 32 2.571212 GACACAAATCACCACAGACCA 58.429 47.619 0.00 0.00 0.00 4.02
32 33 1.880027 GGACACAAATCACCACAGACC 59.120 52.381 0.00 0.00 0.00 3.85
33 34 1.531149 CGGACACAAATCACCACAGAC 59.469 52.381 0.00 0.00 0.00 3.51
34 35 1.542328 CCGGACACAAATCACCACAGA 60.542 52.381 0.00 0.00 0.00 3.41
35 36 0.874390 CCGGACACAAATCACCACAG 59.126 55.000 0.00 0.00 0.00 3.66
36 37 0.181587 ACCGGACACAAATCACCACA 59.818 50.000 9.46 0.00 0.00 4.17
37 38 0.591170 CACCGGACACAAATCACCAC 59.409 55.000 9.46 0.00 0.00 4.16
38 39 0.536233 CCACCGGACACAAATCACCA 60.536 55.000 9.46 0.00 0.00 4.17
39 40 1.241315 CCCACCGGACACAAATCACC 61.241 60.000 9.46 0.00 0.00 4.02
40 41 1.862602 GCCCACCGGACACAAATCAC 61.863 60.000 9.46 0.00 0.00 3.06
41 42 1.602323 GCCCACCGGACACAAATCA 60.602 57.895 9.46 0.00 0.00 2.57
42 43 2.686816 CGCCCACCGGACACAAATC 61.687 63.158 9.46 0.00 0.00 2.17
43 44 2.671619 CGCCCACCGGACACAAAT 60.672 61.111 9.46 0.00 0.00 2.32
71 72 4.179579 GCAAAGCGCGGATGACCC 62.180 66.667 8.83 0.00 0.00 4.46
72 73 4.179579 GGCAAAGCGCGGATGACC 62.180 66.667 8.83 9.91 43.84 4.02
73 74 2.855728 CTTGGCAAAGCGCGGATGAC 62.856 60.000 8.83 10.99 43.84 3.06
74 75 2.671276 TTGGCAAAGCGCGGATGA 60.671 55.556 8.83 0.00 43.84 2.92
75 76 2.202518 CTTGGCAAAGCGCGGATG 60.203 61.111 8.83 3.48 43.84 3.51
83 84 2.049802 CACGGCAGCTTGGCAAAG 60.050 61.111 0.00 0.00 43.94 2.77
84 85 3.604667 CCACGGCAGCTTGGCAAA 61.605 61.111 0.00 0.00 43.94 3.68
85 86 4.892965 ACCACGGCAGCTTGGCAA 62.893 61.111 12.26 0.00 43.94 4.52
86 87 4.892965 AACCACGGCAGCTTGGCA 62.893 61.111 12.26 0.00 43.94 4.92
87 88 4.347453 CAACCACGGCAGCTTGGC 62.347 66.667 12.26 1.16 39.85 4.52
88 89 3.673484 CCAACCACGGCAGCTTGG 61.673 66.667 11.07 11.07 39.00 3.61
96 97 1.068434 AGAAACAAATGCCAACCACGG 59.932 47.619 0.00 0.00 0.00 4.94
97 98 2.507339 AGAAACAAATGCCAACCACG 57.493 45.000 0.00 0.00 0.00 4.94
98 99 4.058721 AGAAGAAACAAATGCCAACCAC 57.941 40.909 0.00 0.00 0.00 4.16
99 100 4.405358 AGAAGAAGAAACAAATGCCAACCA 59.595 37.500 0.00 0.00 0.00 3.67
100 101 4.948847 AGAAGAAGAAACAAATGCCAACC 58.051 39.130 0.00 0.00 0.00 3.77
101 102 6.908870 AAAGAAGAAGAAACAAATGCCAAC 57.091 33.333 0.00 0.00 0.00 3.77
102 103 7.920160 AAAAAGAAGAAGAAACAAATGCCAA 57.080 28.000 0.00 0.00 0.00 4.52
123 124 3.583806 CAGCACAACACACCAAGAAAAA 58.416 40.909 0.00 0.00 0.00 1.94
124 125 2.673610 GCAGCACAACACACCAAGAAAA 60.674 45.455 0.00 0.00 0.00 2.29
125 126 1.135141 GCAGCACAACACACCAAGAAA 60.135 47.619 0.00 0.00 0.00 2.52
126 127 0.455410 GCAGCACAACACACCAAGAA 59.545 50.000 0.00 0.00 0.00 2.52
127 128 0.394216 AGCAGCACAACACACCAAGA 60.394 50.000 0.00 0.00 0.00 3.02
128 129 0.029834 GAGCAGCACAACACACCAAG 59.970 55.000 0.00 0.00 0.00 3.61
129 130 1.713937 CGAGCAGCACAACACACCAA 61.714 55.000 0.00 0.00 0.00 3.67
130 131 2.179547 CGAGCAGCACAACACACCA 61.180 57.895 0.00 0.00 0.00 4.17
131 132 2.633657 CGAGCAGCACAACACACC 59.366 61.111 0.00 0.00 0.00 4.16
152 153 3.953766 ACATCGAGTACAGATAACGCTG 58.046 45.455 0.00 0.00 41.63 5.18
153 154 4.352039 CAACATCGAGTACAGATAACGCT 58.648 43.478 0.00 0.00 0.00 5.07
154 155 3.486108 CCAACATCGAGTACAGATAACGC 59.514 47.826 0.00 0.00 0.00 4.84
155 156 4.669318 ACCAACATCGAGTACAGATAACG 58.331 43.478 0.00 0.00 0.00 3.18
156 157 5.220416 GCAACCAACATCGAGTACAGATAAC 60.220 44.000 0.00 0.00 0.00 1.89
157 158 4.868171 GCAACCAACATCGAGTACAGATAA 59.132 41.667 0.00 0.00 0.00 1.75
158 159 4.159693 AGCAACCAACATCGAGTACAGATA 59.840 41.667 0.00 0.00 0.00 1.98
159 160 3.055819 AGCAACCAACATCGAGTACAGAT 60.056 43.478 0.00 0.00 0.00 2.90
160 161 2.299013 AGCAACCAACATCGAGTACAGA 59.701 45.455 0.00 0.00 0.00 3.41
161 162 2.688507 AGCAACCAACATCGAGTACAG 58.311 47.619 0.00 0.00 0.00 2.74
162 163 2.831685 AGCAACCAACATCGAGTACA 57.168 45.000 0.00 0.00 0.00 2.90
163 164 3.364964 CCAAAGCAACCAACATCGAGTAC 60.365 47.826 0.00 0.00 0.00 2.73
164 165 2.811431 CCAAAGCAACCAACATCGAGTA 59.189 45.455 0.00 0.00 0.00 2.59
165 166 1.608590 CCAAAGCAACCAACATCGAGT 59.391 47.619 0.00 0.00 0.00 4.18
166 167 1.879380 TCCAAAGCAACCAACATCGAG 59.121 47.619 0.00 0.00 0.00 4.04
167 168 1.974265 TCCAAAGCAACCAACATCGA 58.026 45.000 0.00 0.00 0.00 3.59
168 169 2.791383 TTCCAAAGCAACCAACATCG 57.209 45.000 0.00 0.00 0.00 3.84
169 170 5.132897 TGTATTCCAAAGCAACCAACATC 57.867 39.130 0.00 0.00 0.00 3.06
170 171 5.543507 TTGTATTCCAAAGCAACCAACAT 57.456 34.783 0.00 0.00 0.00 2.71
171 172 5.344743 TTTGTATTCCAAAGCAACCAACA 57.655 34.783 0.00 0.00 38.12 3.33
181 182 1.075698 TCCCCCGCTTTGTATTCCAAA 59.924 47.619 0.00 0.00 40.71 3.28
182 183 0.699399 TCCCCCGCTTTGTATTCCAA 59.301 50.000 0.00 0.00 0.00 3.53
183 184 0.699399 TTCCCCCGCTTTGTATTCCA 59.301 50.000 0.00 0.00 0.00 3.53
184 185 1.475280 GTTTCCCCCGCTTTGTATTCC 59.525 52.381 0.00 0.00 0.00 3.01
185 186 1.475280 GGTTTCCCCCGCTTTGTATTC 59.525 52.381 0.00 0.00 0.00 1.75
186 187 1.552578 GGTTTCCCCCGCTTTGTATT 58.447 50.000 0.00 0.00 0.00 1.89
187 188 0.323999 GGGTTTCCCCCGCTTTGTAT 60.324 55.000 0.00 0.00 45.80 2.29
188 189 1.075305 GGGTTTCCCCCGCTTTGTA 59.925 57.895 0.00 0.00 45.80 2.41
189 190 2.203582 GGGTTTCCCCCGCTTTGT 60.204 61.111 0.00 0.00 45.80 2.83
198 199 3.615592 GCATTACCGAAAAAGGGTTTCCC 60.616 47.826 0.00 0.00 45.90 3.97
199 200 3.006003 TGCATTACCGAAAAAGGGTTTCC 59.994 43.478 0.00 0.00 38.99 3.13
200 201 4.245845 TGCATTACCGAAAAAGGGTTTC 57.754 40.909 0.00 0.00 38.99 2.78
201 202 4.562552 CCATGCATTACCGAAAAAGGGTTT 60.563 41.667 0.00 0.00 38.99 3.27
202 203 3.056179 CCATGCATTACCGAAAAAGGGTT 60.056 43.478 0.00 0.00 38.99 4.11
203 204 2.495669 CCATGCATTACCGAAAAAGGGT 59.504 45.455 0.00 0.00 41.62 4.34
204 205 2.495669 ACCATGCATTACCGAAAAAGGG 59.504 45.455 0.00 0.00 35.02 3.95
205 206 3.866883 ACCATGCATTACCGAAAAAGG 57.133 42.857 0.00 0.00 37.30 3.11
206 207 5.890334 ACATACCATGCATTACCGAAAAAG 58.110 37.500 0.00 0.00 0.00 2.27
207 208 5.906113 ACATACCATGCATTACCGAAAAA 57.094 34.783 0.00 0.00 0.00 1.94
208 209 5.184096 ACAACATACCATGCATTACCGAAAA 59.816 36.000 0.00 0.00 0.00 2.29
209 210 4.702612 ACAACATACCATGCATTACCGAAA 59.297 37.500 0.00 0.00 0.00 3.46
210 211 4.095632 CACAACATACCATGCATTACCGAA 59.904 41.667 0.00 0.00 0.00 4.30
211 212 3.625313 CACAACATACCATGCATTACCGA 59.375 43.478 0.00 0.00 0.00 4.69
212 213 3.625313 TCACAACATACCATGCATTACCG 59.375 43.478 0.00 0.00 0.00 4.02
213 214 4.881273 TCTCACAACATACCATGCATTACC 59.119 41.667 0.00 0.00 0.00 2.85
245 246 6.537453 AACAGATGTAGTAGCACTGATTCT 57.463 37.500 0.00 0.00 33.53 2.40
256 257 9.865321 GTGTTGGAGTATTTAACAGATGTAGTA 57.135 33.333 0.00 0.00 35.24 1.82
320 321 5.695816 GCTATTCATGCTTCTCTGTTCCTAG 59.304 44.000 0.00 0.00 0.00 3.02
386 423 3.359033 ACAAGTATGGCATGCTGTTCAT 58.641 40.909 18.99 14.42 35.31 2.57
419 456 2.704065 ACGGAGGGAGTACATATTTGGG 59.296 50.000 0.00 0.00 0.00 4.12
424 461 3.614568 AGGAACGGAGGGAGTACATAT 57.385 47.619 0.00 0.00 0.00 1.78
426 463 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
428 465 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
429 466 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
431 468 6.569994 CGACTTATATTTAGGAACGGAGGGAG 60.570 46.154 0.00 0.00 0.00 4.30
432 469 5.242393 CGACTTATATTTAGGAACGGAGGGA 59.758 44.000 0.00 0.00 0.00 4.20
434 471 6.081872 ACGACTTATATTTAGGAACGGAGG 57.918 41.667 0.00 0.00 0.00 4.30
435 472 7.998753 AAACGACTTATATTTAGGAACGGAG 57.001 36.000 0.00 0.00 0.00 4.63
437 474 9.520204 TCTAAAACGACTTATATTTAGGAACGG 57.480 33.333 0.00 0.00 36.48 4.44
452 489 9.968870 GTCTATATTGGAATCTCTAAAACGACT 57.031 33.333 0.00 0.00 0.00 4.18
453 490 9.968870 AGTCTATATTGGAATCTCTAAAACGAC 57.031 33.333 0.00 0.00 0.00 4.34
461 498 9.179909 CCGTATGTAGTCTATATTGGAATCTCT 57.820 37.037 0.00 0.00 0.00 3.10
462 499 9.175312 TCCGTATGTAGTCTATATTGGAATCTC 57.825 37.037 7.43 0.00 0.00 2.75
463 500 9.179909 CTCCGTATGTAGTCTATATTGGAATCT 57.820 37.037 9.87 0.00 0.00 2.40
464 501 7.916450 GCTCCGTATGTAGTCTATATTGGAATC 59.084 40.741 9.87 4.29 0.00 2.52
465 502 7.396339 TGCTCCGTATGTAGTCTATATTGGAAT 59.604 37.037 9.87 0.00 0.00 3.01
466 503 6.717997 TGCTCCGTATGTAGTCTATATTGGAA 59.282 38.462 9.87 0.00 0.00 3.53
467 504 6.243148 TGCTCCGTATGTAGTCTATATTGGA 58.757 40.000 8.84 8.84 0.00 3.53
468 505 6.510879 TGCTCCGTATGTAGTCTATATTGG 57.489 41.667 0.00 0.00 0.00 3.16
469 506 8.812147 TTTTGCTCCGTATGTAGTCTATATTG 57.188 34.615 0.00 0.00 0.00 1.90
470 507 9.424319 CATTTTGCTCCGTATGTAGTCTATATT 57.576 33.333 0.00 0.00 0.00 1.28
471 508 8.803235 TCATTTTGCTCCGTATGTAGTCTATAT 58.197 33.333 0.00 0.00 0.00 0.86
472 509 8.173542 TCATTTTGCTCCGTATGTAGTCTATA 57.826 34.615 0.00 0.00 0.00 1.31
473 510 7.050970 TCATTTTGCTCCGTATGTAGTCTAT 57.949 36.000 0.00 0.00 0.00 1.98
474 511 6.096423 ACTCATTTTGCTCCGTATGTAGTCTA 59.904 38.462 0.00 0.00 0.00 2.59
475 512 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
476 513 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
477 514 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
478 515 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
479 516 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
480 517 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
481 518 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
482 519 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
483 520 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
484 521 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
485 522 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
486 523 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
487 524 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
519 556 9.729281 TGAACTACATACGGATGTATATAGACA 57.271 33.333 20.64 12.87 45.42 3.41
528 565 9.778741 ATTTCAATATGAACTACATACGGATGT 57.221 29.630 19.12 19.12 43.12 3.06
531 568 9.692749 GAGATTTCAATATGAACTACATACGGA 57.307 33.333 0.00 0.00 43.12 4.69
532 569 9.698309 AGAGATTTCAATATGAACTACATACGG 57.302 33.333 0.00 0.00 43.12 4.02
553 590 9.057089 CGTTCCTAAATATGCCTTTTTAGAGAT 57.943 33.333 11.59 0.00 37.53 2.75
554 591 7.497909 CCGTTCCTAAATATGCCTTTTTAGAGA 59.502 37.037 11.59 6.39 37.53 3.10
555 592 7.497909 TCCGTTCCTAAATATGCCTTTTTAGAG 59.502 37.037 11.59 4.74 37.53 2.43
556 593 7.340256 TCCGTTCCTAAATATGCCTTTTTAGA 58.660 34.615 11.59 0.00 37.53 2.10
557 594 7.255139 CCTCCGTTCCTAAATATGCCTTTTTAG 60.255 40.741 5.40 5.40 35.92 1.85
558 595 6.544564 CCTCCGTTCCTAAATATGCCTTTTTA 59.455 38.462 0.00 0.00 0.00 1.52
559 596 5.359860 CCTCCGTTCCTAAATATGCCTTTTT 59.640 40.000 0.00 0.00 0.00 1.94
560 597 4.887655 CCTCCGTTCCTAAATATGCCTTTT 59.112 41.667 0.00 0.00 0.00 2.27
561 598 4.165372 TCCTCCGTTCCTAAATATGCCTTT 59.835 41.667 0.00 0.00 0.00 3.11
562 599 3.714798 TCCTCCGTTCCTAAATATGCCTT 59.285 43.478 0.00 0.00 0.00 4.35
563 600 3.314693 TCCTCCGTTCCTAAATATGCCT 58.685 45.455 0.00 0.00 0.00 4.75
564 601 3.764237 TCCTCCGTTCCTAAATATGCC 57.236 47.619 0.00 0.00 0.00 4.40
565 602 4.704965 ACTTCCTCCGTTCCTAAATATGC 58.295 43.478 0.00 0.00 0.00 3.14
566 603 7.097834 GGATACTTCCTCCGTTCCTAAATATG 58.902 42.308 0.00 0.00 39.14 1.78
567 604 6.785963 TGGATACTTCCTCCGTTCCTAAATAT 59.214 38.462 0.00 0.00 43.07 1.28
568 605 6.138263 TGGATACTTCCTCCGTTCCTAAATA 58.862 40.000 0.00 0.00 43.07 1.40
569 606 4.966805 TGGATACTTCCTCCGTTCCTAAAT 59.033 41.667 0.00 0.00 43.07 1.40
570 607 4.355549 TGGATACTTCCTCCGTTCCTAAA 58.644 43.478 0.00 0.00 43.07 1.85
571 608 3.985127 TGGATACTTCCTCCGTTCCTAA 58.015 45.455 0.00 0.00 43.07 2.69
572 609 3.675348 TGGATACTTCCTCCGTTCCTA 57.325 47.619 0.00 0.00 43.07 2.94
573 610 2.544844 TGGATACTTCCTCCGTTCCT 57.455 50.000 0.00 0.00 43.07 3.36
574 611 3.840124 AATGGATACTTCCTCCGTTCC 57.160 47.619 0.00 0.00 43.07 3.62
575 612 7.803279 AATTAAATGGATACTTCCTCCGTTC 57.197 36.000 0.00 0.00 40.37 3.95
576 613 9.862149 ATAAATTAAATGGATACTTCCTCCGTT 57.138 29.630 0.00 0.00 42.52 4.44
577 614 9.862149 AATAAATTAAATGGATACTTCCTCCGT 57.138 29.630 0.00 0.00 43.07 4.69
625 662 5.363580 AGAAAGGCTGGAAATTTTCTGTTCA 59.636 36.000 8.93 0.00 38.18 3.18
663 707 2.255252 CCGCTTTTCACTTGGGCG 59.745 61.111 0.00 0.00 44.48 6.13
678 722 0.958091 TGAGCACCAAAAATGGACCG 59.042 50.000 1.10 0.00 0.00 4.79
782 827 1.730501 TGGAGCAGAGCTTTCATTCG 58.269 50.000 0.00 0.00 39.88 3.34
856 904 2.426738 AGTCTATCTCTCTGTGCAGTGC 59.573 50.000 8.58 8.58 0.00 4.40
857 905 3.181488 CCAGTCTATCTCTCTGTGCAGTG 60.181 52.174 0.00 0.00 0.00 3.66
866 915 4.156008 GCTAAGCTAGCCAGTCTATCTCTC 59.844 50.000 12.13 0.00 45.95 3.20
937 986 5.017490 TCTTGACTCCTAAGGTAGAACAGG 58.983 45.833 0.00 0.00 0.00 4.00
955 1004 7.181305 TCTCTCTCTACCTTCTACTCTTCTTGA 59.819 40.741 0.00 0.00 0.00 3.02
956 1005 7.335627 TCTCTCTCTACCTTCTACTCTTCTTG 58.664 42.308 0.00 0.00 0.00 3.02
957 1006 7.402071 TCTCTCTCTCTACCTTCTACTCTTCTT 59.598 40.741 0.00 0.00 0.00 2.52
958 1007 6.901300 TCTCTCTCTCTACCTTCTACTCTTCT 59.099 42.308 0.00 0.00 0.00 2.85
959 1008 7.120923 TCTCTCTCTCTACCTTCTACTCTTC 57.879 44.000 0.00 0.00 0.00 2.87
960 1009 6.672657 ACTCTCTCTCTCTACCTTCTACTCTT 59.327 42.308 0.00 0.00 0.00 2.85
962 1011 6.097839 TCACTCTCTCTCTCTACCTTCTACTC 59.902 46.154 0.00 0.00 0.00 2.59
963 1012 5.962031 TCACTCTCTCTCTCTACCTTCTACT 59.038 44.000 0.00 0.00 0.00 2.57
964 1013 6.229936 TCACTCTCTCTCTCTACCTTCTAC 57.770 45.833 0.00 0.00 0.00 2.59
990 1039 0.985490 AGTCCTGCATCTTCTCCCCC 60.985 60.000 0.00 0.00 0.00 5.40
991 1040 0.179936 CAGTCCTGCATCTTCTCCCC 59.820 60.000 0.00 0.00 0.00 4.81
992 1041 0.179936 CCAGTCCTGCATCTTCTCCC 59.820 60.000 0.00 0.00 0.00 4.30
1125 1174 0.031314 CGGAGTGGACGATGATGGAG 59.969 60.000 0.00 0.00 0.00 3.86
1238 1287 3.285484 GTTCAGCTGATGGATGGATGTT 58.715 45.455 19.04 0.00 31.38 2.71
1239 1288 2.240414 TGTTCAGCTGATGGATGGATGT 59.760 45.455 19.04 0.00 31.38 3.06
1298 1349 8.412456 CACTATTATGCATGAACCCACATAAAA 58.588 33.333 10.16 0.00 38.20 1.52
1302 1353 5.448654 ACACTATTATGCATGAACCCACAT 58.551 37.500 10.16 0.00 0.00 3.21
1373 1426 2.893489 AGCAAAGAACCAGTTTCATCCC 59.107 45.455 0.00 0.00 36.57 3.85
1451 1504 5.927689 GGAAATGCAAACAATCTGAATGACA 59.072 36.000 0.00 0.00 0.00 3.58
1647 1718 4.201695 GCGTTTCTTTTAGGACGAGGAATC 60.202 45.833 0.00 0.00 37.69 2.52
1774 1849 3.647590 ACAAGGATGGAGGTTGCAAAATT 59.352 39.130 0.00 0.00 0.00 1.82
1781 1858 3.423539 TCTGAACAAGGATGGAGGTTG 57.576 47.619 0.00 0.00 0.00 3.77
1887 1974 3.395639 CAAACCCTCTGTTAACTACGCA 58.604 45.455 7.22 0.00 35.67 5.24
1895 1982 2.036733 CTCGACACCAAACCCTCTGTTA 59.963 50.000 0.00 0.00 35.67 2.41
1897 1984 0.393077 CTCGACACCAAACCCTCTGT 59.607 55.000 0.00 0.00 0.00 3.41
1898 1985 0.393077 ACTCGACACCAAACCCTCTG 59.607 55.000 0.00 0.00 0.00 3.35
1931 2024 2.627510 AAAAGCCAACACAGCACCGC 62.628 55.000 0.00 0.00 0.00 5.68
1991 2087 1.691196 TTGTTCCTTTCCTGCACCAG 58.309 50.000 0.00 0.00 0.00 4.00
2022 2118 4.080807 TGTTCCTTTTAGGTCACACTCACA 60.081 41.667 0.00 0.00 36.53 3.58
2066 2169 1.340991 ACACACCAGTTCCAAAGCTGT 60.341 47.619 0.00 0.00 0.00 4.40
2104 2214 5.066117 TCTGCATCATTCTCTGAATTGCTTC 59.934 40.000 14.18 0.00 39.55 3.86
2108 2218 4.576873 AGCTCTGCATCATTCTCTGAATTG 59.423 41.667 0.00 0.00 37.44 2.32
2109 2219 4.576873 CAGCTCTGCATCATTCTCTGAATT 59.423 41.667 0.00 0.00 37.44 2.17


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.